U.S. counter-terror organizations have a rather massive problem when it comes to international air and sea traffic. At sea, there are some 30,000 large (10,000 GRT and larger) ocean going ships. While aircraft should be easier to track, since most of those coming into North America do so via a few air corridors, there are actually many more smaller aircraft coming in using a larger number of air routes. There are 300,000 non-military aircraft available worldwide, operating from over 40,000 airfields. While many of these can't make it to North America, they can, in theory, be used to attack American interests (embassies, military bases) overseas.
Keeping track of all these ships and aircraft is impossible. But it is possible to pick out the ships and aircraft that are more likely to be used for terror operations, and keep an eye on those. It's also possible to keep an eye on air and naval smuggling routes, which is apparently one reason that the U.S. Navy has been devoting so many ships and aircraft to this over the last eight years.
While no sea or airborne terrorist attacks have been detected, the U.S. has learned a lot more about smuggling worldwide, and that often involves people, or weapons that could be used by smugglers.